[gmx-users] problem with genconf

[David]

On Thu, 2004-06-10 at 17:03, Albert Sun wrote:
> Thanks, David !
> How to equilibrate with freshly generated velocities?
>  
do an MD simulation!

> Regards,
>  
> 
> David <spoel at xray.bmc.uu.se> wrote:
>         On Wed, 2004-06-09 at 20:45, Albert Sun wrote:
>         > Dear Users.
>         > 
>         > The problem is solved beause I used the same file name in
>         genconf.
>         > 
>         > I have another inquery on genconf. It is said that genconf
>         multiplies
>         > a given coordinate file by simply stacking them on top of
>         each other,
>         > like child playing wood blocks. It is OK for positions of
>         atoms. 
>         > However, I found the velocity for all blocks are exactly the
>         same, is
>         > it correct ?
>         just equilibrate for a while with freshly generated
>         velocities. if you
>         have a lot of order in your original system you may need to
>         equilibrate
>         long.
>         > 
>         > Thanks in advance.
>         > 
>         > Regards,
>         > 
>         > Albert. 
>         > 
>         > 
>         > 
>         >
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>         -- 
>         David.
>         ________________________________________________________________________
>         David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
>         group,
>         Dept. of Cell and Molecular Biology, Uppsala University.
>         Husargatan 3, Box 596, 75124 Uppsala, Sweden
>         phone: 46 18 471 4205 fax: 46 18 511 755
>         spoel at xray.bmc.uu.se spoel at gromacs.org
>         http://xray.bmc.uu.se/~spoel
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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